Firewall won't open or close ports

Now.... a slight problem - when I open or close ports in the Tools section of ISPConfig, it doesnt seem to have any effect on the actual firewall (I found this out by doing a portscan)

In the Firewall section I have Port 5060 open (for a VOIP system) however when i do a portscan it says it's closed. I've also tried to turn off port 873 (Rsync) but when I do the scan it says that one is open... I can't seem to win!

If someone could help me out here that would be great... Oh, and I'm new to linux (Debian) so you might have to be a bit specific... sorry!